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Sample GSM1517647

Query DataSets for GSM1517647

Status

Public on Jan 21, 2015

Title

rep1_input

Sample type

SRA

Source name

2-5mm tassel primordia

Organism

Zea mays

Characteristics

chip antibody: input
tissue: 2-5mm tassel primordia
experiment: ChIPseq
genotype: normal B73

Treatment protocol

These experiments used families containing a transgene integration event that complemented the mutant (A399S1-7), and expression of the transgene was verified by fluorescence microscopy.

Growth protocol

Developing tassel primordia, approximately 2-5mm in size, were harvested from FEA4-YFP plants grown in the field at CSHL uplands farm facility.

Extracted molecule

genomic DNA

Extraction protocol

Following dissection, inflorescences were immediately cross-linked in buffer containing 1% formaldehyde for 15 minutes under vacuum, followed by addition of glycine to a concentration of 0.1 M, which was infiltrated for 5 minutes. Following three washes with distilled water, the cross-linked tissues were dried with paper towels and flash frozen in liquid nitrogen.
Chromatin extracts from YFP-FEA4 plants were immunoprecipitated with anti-GFP (ab290, Abcam) antibody. Protein A dynabeads (Invitrogen) blocked with yeast tRNA and BSA were used to capture antibody-chromatin complexes (Morohashi et al., 2012). Following purification of immunoprecipitated DNA, libraries were constructed using the Ovation Low Input DR kit (Nugen) and barcoded to allow multiplexed sequencing. Two input and two IP libraries were sequenced on one run of an Illumina MiSeq machine.

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina MiSeq

Description

rep1_FEA4_MACS_peaks.bed
rep1_FEA4_MACS_summits.bed

Data processing

Libraries were quantified on an Agilent bioanalyzer (Agilent) using a DNA 1000 chip, and sequenced using the Illumina MiSeq platform at the CSHL Genome Center.
All image processing and base calling was done with the Illumina Real Time Analysis software as the run progressed. Binary basecall files were then transferred to a shared Linux server for further processing and archival. The latest version of the Illumina processing software CASAVA was used to generate fastq files.
ChIP-seq reads were aligned to the maize reference genome (AGPv2) using Bowtie (v.0.12.7;(Langmead et al., 2009)) and peak calling was performed with MACS version 1.4.0rc2 using only uniquely mapped reads (Zhang et al., 2008). Peaks were identified as significantly enriched (p<1e-05) in each of the ChIP-seq libraries compared to input DNA.
Genome_build: Zea mays refgen_agpv2
Supplementary_files_format_and_content: Processed data files are output of MACS.1.4.0rc2. The peaks.bed file includes (from left to right columns) chromosome, peak start, peak stop, -10*log10(pval). The summits.bed file includes (from left to right columns) chromosome, summit start, summit stop, tag pileup at summit.

Submission date

Oct 01, 2014

Last update date

May 15, 2019

Contact name

Andrea L Eveland

E-mail(s)

[email protected]

Organization name

Donald Danforth Plant Science Center

Street address

975 N. Warson Road